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SARS-CoV-2 Papain-like Protease (PLpro) in complex with Fragment 53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WRH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 50 mM HEPES pH = 7.0, Tryptone 2-4 % w/v and 10-16 % PEG-3350
12 mg/mL protein
1:1 drop ratio
cocrystalised with weak affinity ligand then back soaked with ligand of interest
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.167 α = 90 b = 78.167 β = 90 c = 231.464 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2023-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0006 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 46.29 100 0.045 0.046 0.01 1 41.5 20.2 39922 32.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 100 1.244 1.274 0.274 0.89 3.1 20.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 39.08 1.33 39812 1906 99.98 0.2089 0.207 0.2078 0.2482 0.248 39.27
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.2941 f_angle_d 1.4223 f_chiral_restr 0.0566 f_plane_restr 0.0079 f_bond_d 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing